Schema for refFlat
  Database: sarHar1    Primary Table: refFlat    Row Count: 72   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName MIR216Bvarchar(255) values Name of gene as it appears in genome browser.
name NR_105683varchar(255) values Name of gene
chrom chr1_GL834734_randomvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1003763int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1003913int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1003913int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1003913int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 1003763,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1003913,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      hgFixed.gbCdnaInfo.acc (via refFlat.name)
      hgFixed.gbSeq.acc (via refFlat.name)
      hgFixed.imageClone.acc (via refFlat.name)
      hgFixed.refLink.mrnaAcc (via refFlat.name)
      hgFixed.refSeqStatus.mrnaAcc (via refFlat.name)
      hgFixed.refSeqSummary.mrnaAcc (via refFlat.name)
      knownGeneV39.kgXref.refseq (via refFlat.name)
      knownGeneV39.knownToRefSeq.value (via refFlat.name)
      sarHar1.mrnaOrientInfo.name (via refFlat.name)
      sarHar1.refGene.name (via refFlat.name)
      sarHar1.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
MIR216BNR_105683chr1_GL834734_random+100376310039131003913100391311003763,1003913,
MIR340NR_105682chr1_GL834730_random+7410117411617411617411611741011,741161,
MIR140NR_105685chr1_GL834769_random+190949919096491909649190964911909499,1909649,
MIR216ANR_105684chr1_GL834734_random+101994110200911020091102009111019941,1020091,
MIR202NR_105687chr1_GL835536_random+1203981205481205481205481120398,120548,
MIR126NR_105686chr1_GL834949_random+422143714371437114221,4371,
MIR133ANR_105690chr2_GL841304_random+6927036928536928536928531692703,692853,
MIR1540NR_105688chr1_GL836570_random+10619107691076910769110619,10769,
MIR9NR_105689chr2_GL841279_random+9265169266669266669266661926516,926666,
MIR7NR_105700chr2_GL841540_random+252866825288182528818252881812528668,2528818,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.